{"id":5559,"date":"2023-09-04T03:08:16","date_gmt":"2023-09-04T03:08:16","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-collection\/sln-breast\/"},"modified":"2023-09-13T11:57:13","modified_gmt":"2023-09-13T11:57:13","slug":"sln-breast","status":"publish","type":"tcia_collection","link":"https:\/\/cm.vastapps.dev\/tcia-collection\/sln-breast\/","title":{"rendered":"SLN-BREAST"},"featured_media":0,"template":"","citation-tax":[],"cancer_types":["Breast Cancer"],"citations":[4400,4401,2925],"collection_doi":"10.7937\/tcia.2019.3xbn2jcc","collection_download_info":"<br\/>\nClick the Versions tab for more info about data releases.","collection_downloads":[4946,4947],"full_export":"<h2 id=\"BreastMetastasestoAxillaryLymphNodes(SLNBreast)-Summary\">Summary<\/h2><p><br\/><\/p>The detection of breast cancer metastases to lymph nodes is of great prognostic value for patient treatment. Using machine learning to detect metastatic breast cancer to lymph nodes can increase efficiency of pathologist diagnosis and ultimately ensure patients are accurately staged for prospective treatment. This dataset allows for the objective comparison of breast cancer metastases detection algorithms.<\/p><p>The dataset consists of 130 de-identified whole slide images of H&amp;E stained axillary lymph node specimens from 78 patients. Metastatic breast carcinoma is present in 36 of the WSI from 27 patients. No patient inclusion\/exclusion criteria were followed. No slide inclusion\/exclusion criteria were followed. The slides were scanned at Memorial Sloan Kettering Cancer Center (MSKCC) with Leica Aperio AT2 scanners at 20x equivalent magnification (0.5 microns per pixel). Together with the slides, the class label of each slide, either positive or negative for breast carcinoma, is given. The slide class label was obtained from the pathology report of the respective case.<p><br\/><\/p><div class=\"tab-style-builtin\"><div class=\"localtabs-macro\"><div class=\"aui-tabs horizontal-tabs\" role=\"application\" data-aui-responsive=\"true\"><ul class=\"tabs-menu\"><li class=\"menu-item bv-localtab  active-tab \"><a href=\"#5276333988adbefa280e46f4ac66f26e5cbb5359\"><strong>Data Access<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#5276333970d68d4b9cbb42a5890ac7b4eef58bb9\"><strong>Detailed Description<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#52763339f8eb47bb0a5c4c16a653b27ea96c7ec9\"><strong>Citations &amp; Data Usage Policy<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#527633392e5aefb75742405e85642c6b7c2c8f52\"><strong>Versions<\/strong><\/a> <\/li><\/ul><div class=\"tabs-pane  active-pane \" id=\"5276333988adbefa280e46f4ac66f26e5cbb5359\" active=\"true\" name=\"Data Access\" ><h3 id=\"BreastMetastasestoAxillaryLymphNodes(SLNBreast)-DataAccess\">Data Access<\/h3><div class=\"table-wrap\"><table class=\"wrapped relative-table confluenceTable\" style=\"width: 49.8196%;\"><colgroup><col style=\"width: 29.7284%;\"\/><col style=\"width: 40.5034%;\"\/><col style=\"width: 29.738%;\"\/><\/colgroup><tbody><tr><th class=\"confluenceTh\">Data Type<\/th><th class=\"confluenceTh\">Download all or Query\/Filter<\/th><th class=\"confluenceTh\">License<\/th><\/tr><tr><td class=\"confluenceTd\">Images (.SVS, 53 GB)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/71?passcode=79b9a8885b0115c3c0d061d3954d2f78087637e5\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/pathdb.cancerimagingarchive.net\/imagesearch?f%5B0%5D=collection:sln_breast\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/71?passcode=79b9a8885b0115c3c0d061d3954d2f78087637e5\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a><\/p><p>(Download and apply the\u00a0<a href=\"https:\/\/www.ibm.com\/aspera\/connect\/\" class=\"external-link\" rel=\"nofollow\">IBM-Aspera-Connect plugin\u00a0<\/a>to your browser to retrieve this faspex package)\u00a0<\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">Supplemental Data (CSV)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/52763339\/target.csv?version=1&amp;modificationDate=1563461391272&amp;api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><br\/><\/p><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><p><br\/><\/p><p>Click the Versions tab for more info about data releases.<\/p><\/div><div class=\"tabs-pane \" id=\"5276333970d68d4b9cbb42a5890ac7b4eef58bb9\" name=\"Detailed Description\" ><h3 id=\"BreastMetastasestoAxillaryLymphNodes(SLNBreast)-DetailedDescription\">Detailed Description<\/h3><div class=\"table-wrap\"><table class=\"wrapped confluenceTable\"><colgroup> <col\/> <col\/> <\/colgroup><tbody><tr><th class=\"confluenceTh\"><p>Image Statistics<\/p><\/th><th class=\"confluenceTh\"><br\/><\/th><\/tr><tr><td class=\"confluenceTd\"><p>Modalities<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>Pathology<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Participants<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>78<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Images<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>130<\/p><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Images Size (GB)<\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">53<\/td><\/tr><\/tbody><\/table><\/div><p class=\"auto-cursor-target\"><strong>Explanation of target.csv files<\/strong><\/p><p>target.csv contains a binary label for each slide image in the dataset.<\/p><ul><li>target=1 means that the image contains breast cancer metastases.<\/li><li>target=0 means that the image does not contain breast cancer metastases.<\/li><\/ul><\/div><div class=\"tabs-pane \" id=\"52763339f8eb47bb0a5c4c16a653b27ea96c7ec9\" name=\"Citations BITVOODOO_ANDamp; Data Usage Policy\" ><h3 id=\"BreastMetastasestoAxillaryLymphNodes(SLNBreast)-Citations&amp;DataUsagePolicy\">Citations &amp; Data Usage Policy<\/h3><p class=\"auto-cursor-target\">\n<p>\nUsers must abide by the <a href=\"https:\/\/wiki.cancerimagingarchive.net\/x\/c4hF\" class=\"external-link\" rel=\"nofollow\">TCIA Data Usage Policy and Restrictions<\/a>. Attribution should include references to the following citations:\n<\/p><\/p><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Data Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p><span style=\"color: rgb(51,51,51);text-decoration: none;\">Campanella, G., Hanna, M. G., Brogi, E., &amp; Fuchs, T. J. (2019). <strong>Breast Metastases to Axillary Lymph Nodes [Data set]<\/strong>. The Cancer Imaging Archive. <a href=\"https:\/\/doi.org\/10.7937\/tcia.2019.3xbn2jcc\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.7937\/tcia.2019.3xbn2jcc<\/a><\/span><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Publication Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p><span style=\"color: rgb(0,0,0);text-decoration: none;\">Campanella, G., Hanna, M. G., Geneslaw, L., Miraflor, A., Werneck Krauss Silva, V., Busam, K. J., Brogi, E., Reuter, V. E., Klimstra, D. S., &amp; Fuchs, T. J. (2019). <strong>Clinical-grade computational pathology using weakly supervised deep learning on whole slide images.<\/strong> Nature Medicine (Vol. 25, Issue 8, pp. 1301\u20131309). Springer Science and Business Media LLC. <a href=\"https:\/\/doi.org\/10.1038\/s41591-019-0508-1\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1038\/s41591-019-0508-1<\/a><\/span><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">TCIA Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p>Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F.\u00a0<strong>The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository<\/strong>, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. DOI: <a href=\"https:\/\/doi.org\/10.1007\/s10278-013-9622-7\" class=\"external-link\" rel=\"nofollow\">10.1007\/s10278-013-9622-7<\/a><\/p><\/div><\/div><h3 id=\"BreastMetastasestoAxillaryLymphNodes(SLNBreast)-OtherPublicationsUsingThisData\">Other Publications Using This Data<\/h3><p><span>TCIA maintains<\/span> <a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\" class=\"external-link\" rel=\"nofollow\"> a list of publications<\/a> <span> which leverage TCIA data. <\/span> If you have a manuscript you'd like to add please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\" class=\"external-link\" rel=\"nofollow\"> contact the TCIA Helpdesk<\/a>.<\/p><\/div><div class=\"tabs-pane \" id=\"527633392e5aefb75742405e85642c6b7c2c8f52\" name=\"Versions\" ><h3 id=\"BreastMetastasestoAxillaryLymphNodes(SLNBreast)-Version1(Current):Updated2019\/07\/18\">Version 1 (Current): Updated 2019\/07\/18<\/h3><div class=\"table-wrap\"><table class=\"wrapped fixed-width confluenceTable\" style=\"width: 39.792%;\"><colgroup> <col style=\"width: 47.0017%;\"\/> <col style=\"width: 52.9761%;\"\/> <\/colgroup><tbody><tr><th class=\"confluenceTh\"><span>Data Type<\/span><\/th><th class=\"confluenceTh\"><span>Download all or Query\/Filter<\/span><\/th><\/tr><tr><td class=\"confluenceTd\"><span>Images (.SVS, 53 GB)<\/span><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/71?passcode=79b9a8885b0115c3c0d061d3954d2f78087637e5\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/pathdb.cancerimagingarchive.net\/imagesearch?f%5B0%5D=collection:sln_breast\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/71?passcode=79b9a8885b0115c3c0d061d3954d2f78087637e5\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a><\/p><p>(Download and apply the\u00a0<a href=\"https:\/\/www.ibm.com\/aspera\/connect\/\" class=\"external-link\" rel=\"nofollow\">IBM-Aspera-Connect plugin\u00a0<\/a>to your browser to retrieve this faspex package)\u00a0<\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\"><span>Supplemental Data (CSV)<\/span><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/52763339\/target.csv?version=1&amp;modificationDate=1563461391272&amp;api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><br\/><\/p><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><p><br\/><\/p><\/div><\/div><\/div><\/div><p><br\/><\/p><p><br\/><\/p><p><br\/><\/p><p><br\/><\/p><p><br\/><\/p>","versions":false,"additional_resources":"","cancer_locations":["Breast"],"collection_page_accessibility":"Public","publications_related":"","version_change_log":"","version_change_log_archived":"","analysis_results":"","collection_status":"Complete","publications_using":"TCIA maintains <a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\"> a list of publications<\/a>  which leverage TCIA data.  If you have a manuscript you'd like to add please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\"> contact the TCIA Helpdesk<\/a>.","species":["Human"],"collection_title":"Breast Metastases to Axillary Lymph Nodes","detailed_description":"<strong>Explanation of target.csv files<\/strong>\ntarget.csv contains a binary label for each slide image in the dataset.\n<ul><li>target=1 means that the image contains breast cancer metastases.<\/li><li>target=0 means that the image does not contain breast cancer metastases.<\/li><\/ul>","related_analysis_results":false,"subjects":"78","collection_short_title":"SLN-Breast","data_types":["Pathology"],"date_updated":"2023-09-13","collection_browse_title":"","supporting_data":false,"collection_featured_image":false,"collection_summary":"<br\/>\nThe detection of breast cancer metastases to lymph nodes is of great prognostic value for patient treatment. Using machine learning to detect metastatic breast cancer to lymph nodes can increase efficiency of pathologist diagnosis and ultimately ensure patients are accurately staged for prospective treatment. This dataset allows for the objective comparison of breast cancer metastases detection algorithms.<p>The dataset consists of 130 de-identified whole slide images of H&amp;E stained axillary lymph node specimens from 78 patients. Metastatic breast carcinoma is present in 36 of the WSI from 27 patients. No patient inclusion\/exclusion criteria were followed. No slide inclusion\/exclusion criteria were followed. The slides were scanned at Memorial Sloan Kettering Cancer Center (MSKCC) with Leica Aperio AT2 scanners at 20x equivalent magnification (0.5 microns per pixel). Together with the slides, the class label of each slide, either positive or negative for breast carcinoma, is given. The slide class label was obtained from the pathology report of the respective case.<\/p>\n<br\/>","collection_acknowledgements":"","collection_funding":"","hide_from_browse_table":[],"_links":{"self":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections\/5559"}],"collection":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections"}],"about":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/types\/tcia_collection"}],"wp:attachment":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media?parent=5559"}],"wp:term":[{"taxonomy":"tcia_citation_tax","embeddable":true,"href":"https:\/\/cm.vastapps.dev\/api\/v1\/citation-tax?post=5559"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}